Kumar, M., Tibocha-Bonilla, J. D., Füssy, Z., Lieng, C., Schwenck, S. M., Levesque, A. V., Al-Bassam, M. M., Passi, A., Neal, M., Zuniga, C., Kaiyom, F., Espinoza, J. L., Lim, H., Polson, S. W., Allen, L. Z., & Zengler, K. (2024). Mixotrophic growth of a ubiquitous marine diatom. Science Advances, 10(29), eado2623. https://doi.org/10.1126/sciadv.ado2623

Kolody, B. C., Smith, S. R., Zeigler Allen, L., McCrow, J. P., Moustafa, A., Shi, D., Hopkinson, B. M., Morel, F. M. M., Ward, B. B., & Allen, A. E. (2022). Nitrogen and Iron Availability Drive Metabolic Remodeling and Natural Selection of Diverse Phytoplankton during Experimental Upwelling. MSystems, e00729-22. https://doi.org/10.1128/msystems.00729-22

James, C. C., Barton, A. D., Allen, L. Z., Lampe, R. H., Rabines, A., Schulberg, A., Zheng, H., Goericke, R., Goodwin, K. D., & Allen, A. E. (2022). Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region. Nature Communications, 13(1), 2448. https://doi.org/10.1038/s41467-022-30139-4

Neri, U., Wolf, Y. I., Roux, S., Camargo, A. P., Lee, B., Kazlauskas, D., Chen, I. M., Ivanova, N., Zeigler Allen, L., Paez-Espino, D., Bryant, D. A., Bhaya, D., Krupovic, M., Dolja, V. V., Kyrpides, N. C., Koonin, E. V., Gophna, U., Narrowe, A. B., Probst, A. J., … Wang, Z. (2022). Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell, 185(21), 4023-4037.e18. https://doi.org/10.1016/j.cell.2022.08.023

Oliver, A., Podell, S., Pinowska, A., Traller, J. C., Smith, S. R., McClure, R., Beliaev, A., Bohutskyi, P., Hill, E. A., Rabines, A., Zheng, H., Allen, L. Z., Kuo, A., Grigoriev, I. V., Allen, A. E., Hazlebeck, D., & Allen, E. E. (2021). Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom. Scientific Reports, 11(1), 14. https://doi.org/10.1038/s41598-021-95106-3

Skoog, E. J., Huber, J. A., Serres, M. H., Levesque, A., & Allen, L. Z. (2021). Draft genome sequence of Desulfurobacterium sp. strain AV08, a thermophilic chemolithoautotroph isolated from a deep-sea hydrothermal vent. Microbiology Resource Announcements, 10(34). https://doi.org/ARTN e00615-21 10.1128/MRA.00615-21

Fortunato, C. S., Butterfield, D. A., Larson, B., Lawrence-Slavas, N., Algar, C. K., Allen, L. Z., Holden, J. F., Proskurowski, G., Reddington, E., Stewart, L. C., Topcuoglu, B. D., Vallino, J. J., & Huber, J. A. (2021). Seafloor incubation experiment with deep-sea hydrothermal vent fluid reveals effect of pressure and lag time on autotrophic microbial communities. Applied and Environmental Microbiology, 87(9). https://doi.org/ARTN e00078-21 10.1128/AEM.00078-21

Kolody, B. C., McCrow, J. P., Allen, L. Z., Aylward, F. O., Fontanez, K. M., Moustafa, A., Moniruzzaman, M., Chavez, F. P., Scholin, C. A., Allen, E. E., Worden, A. Z., Delong, E. F., & Allen, A. E. (2019). Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. The ISME Journal. https://doi.org/10.1038/s41396-019-0472-2

Goodwin, K. D., Muller-Karger, F. E., Djurhuus, A., Zeigler Allen, L., Allen, A. E., McCrow, J. P., & Canonico Hyde, G. (2019). Chapter 32 - Molecular Approaches for an Operational Marine Biodiversity Observation Network. In C. Sheppard (Ed.), World Seas: an Environmental Evaluation (Second Edition) (pp. 613–631). Academic Press. https://doi.org/10.1016/B978-0-12-805052-1.00032-2

Roux, S., Adriaenssens, E. M., Dutilh, B. E., Koonin, E. V., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Lavigne, R., Brister, J. R., Varsani, A., Amid, C., Aziz, R. K., Bordenstein, S. R., Bork, P., Breitbart, M., Cochrane, G. R., Daly, R. A., Desnues, C., Duhaime, M. B., … Eloe-Fadrosh, E. A. (2019). Minimum information about an uncultivated virus genome (MIUViG). Nature Biotechnology, 37(1), 29–37. https://doi.org/10.1038/nbt.4306

Zeigler Allen, L., McCrow, J. P., Ininbergs, K., Dupont, C. L., Badger, J. H., Hoffman, J. M., Ekman, M., Allen, A. E., Bergman, B., & Venter, J. C. (2017). The Baltic Sea virome: Diversity and transcriptional activity of DNA and RNA viruses. MSystems, 2. https://doi.org/10.1128/mSystems.00125-16

Llorens-Mares, T., Liu, Z. F., Allen, L. Z., Rusch, D. B., Craig, M. T., Dupont, C. L., Bryant, D. A., & Casamayor, E. O. (2017). Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly. Isme Journal, 11(1), 201–211. https://doi.org/10.1038/ismej.2016.93

Tangherlini, M., Dell’Anno, A., Allen, L. Z., Riccioni, G., & Corinaldesi, C. (2016). Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses. Scientific Reports, 6. https://doi.org/ARTN 28428 10.1038/srep28428

Ma, Y. F., Allen, L. Z., & Palenik, B. (2014). Diversity and genome dynamics of marine cyanophages using metagenomic analyses. Environmental Microbiology Reports, 6(6), 583–594. https://doi.org/10.1111/1758-2229.12160

Dupont, C. L., Larsson, J., Yooseph, S., Ininbergs, K., Goll, J., Asplund-Samuelsson, J., McCrow, J. P., Celepli, N., Allen, L. Z., Ekman, M., Lucas, A. J., Hagstrom, A., Thiagarajan, M., Brindefalk, B., Richter, A. R., Andersson, A. F., Tenney, A., Lundin, D., Tovchigrechko, A., … Bergman, B. (2014). Functional tradeoffs underpin salinity-driven divergence in microbial community composition. PLOS ONE, 9(2). https://doi.org/10.1371/journal.pone.0089549

Yooseph, S., Andrews-Pfannkoch, C., Tenney, A., McQuaid, J., Williamson, S., Thiagarajan, M., Brami, D., Zeigler-Allen, L., Hoffman, J., Goll, J. B., Fadrosh, D., Glass, J., Adams, M. D., Friedman, R., & Venter, J. C. (2013). A metagenomic framework for the study of airborne microbial communities. PLOS ONE, 8(12). https://doi.org/ARTN e81862 10.1371/journal.pone.0081862

Allen, A. E., Allen, L. Z., & McCrow, J. P. (2013). Lineage specific gene family enrichment at the microscale in marine systems. Current Opinion in Microbiology, 16(5), 605–617. https://doi.org/10.1016/j.mib.2013.10.001

Campbell, B. J., Polson, S. W., Allen, L. Z., Williamson, S. J., Lee, C. K., Wommack, K. E., & Cary, S. C. (2013). Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities. Frontiers in Microbiology, 4. https://doi.org/ARTN 182 10.3389/fmicb.2013.00182

Allen, L. Z., Ishoey, T., Novotny, M. A., McLean, J. S., Lasken, R. S., & Williamson, S. J. (2013). Isolation and Genome Analysis of Single Virions using “Single Virus Genomics.” Jove-Journal of Visualized Experiments, 75. https://doi.org/ARTN e3899 10.3791/3899

McLean, J. S., Lombardo, M. J., Ziegler, M. G., Novotny, M., Yee-Greenbaum, J., Badger, J. H., Tesler, G., Nurk, S., Lesin, V., Brami, D., Hall, A. P., Edlund, A., Allen, L. Z., Durkin, S., Reed, S., Torriani, F., Nealson, K. H., Pevzner, P. A., Friedman, R., … Lasken, R. S. (2013). Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform. Genome Research, 23(5), 867–877. https://doi.org/10.1101/gr.150433.112

Smith, M. W., Allen, L. Z., Allen, A. E., Herfort, L., & Simon, H. M. (2013). Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem. Frontiers in Microbiology, 4. https://doi.org/10.3389/Fmicb.2013.00120

Sedghizadeh, P. P., Yooseph, S., Fadrosh, D. W., Zeigler-Allen, L., Thiagarajan, M., Salek, H., Farahnik, F., & Williamson, S. J. (2012). Metagenomic investigation of microbes and viruses in patients with jaw osteonecrosis associated with bisphosphonate therapy. Oral Surgery Oral Medicine Oral Pathology Oral Radiology, 114(6), 764–770. https://doi.org/10.1016/j.oooo.2012.08.444

Williamson, S. J., Allen, L. Z., Lorenzi, H. A., Fadrosh, D. W., Brami, D., Thiagarajan, M., McCrow, J. P., Tovchigrechko, A., Yooseph, S., & Venter, J. C. (2012). Metagenomic Exploration of Viruses throughout the Indian Ocean. PLOS ONE, 7(10). https://doi.org/10.1371/journal.pone.0042047

Allen, L. Z., Allen, E. E., Badger, J. H., McCrow, J. P., Paulsen, I. T., Elbourne, L. D. H., Thiagarajan, M., Rusch, D. B., Nealson, K. H., Williamson, S. J., Venter, J. C., & Allen, A. E. (2012). Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. Isme Journal, 6(7), 1403–1414. https://doi.org/10.1038/ismej.2011.201

McLean, J. S., Fansler, S. J., Majors, P. D., McAteer, K., Allen, L. Z., Shirtliff, M. E., Lux, R., & Shi, W. Y. (2012). Identifying Low pH Active and Lactate-Utilizing Taxa within Oral Microbiome Communities from Healthy Children Using Stable Isotope Probing Techniques. PLOS ONE, 7(3). https://doi.org/ARTN e32219 10.1371/journal.pone.0032219

Eloe, E. A., Fadrosh, D. W., Novotny, M., Allen, L. Z., Kim, M., Lombardo, M. J., Yee-Greenbaum, J., Yooseph, S., Allen, E. E., Lasken, R., Williamson, S. J., & Bartlett, D. H. (2011). Going deeper: Metagenome of a hadopelagic microbial community. PLOS ONE, 6(5). https://doi.org/10.1371/journal.pone.0020388

Allen, L. Z., Ishoey, T., Novotny, M. A., McLean, J. S., Lasken, R. S., & Williamson, S. J. (2011). Single Virus Genomics: A New Tool for Virus Discovery. PLOS ONE, 6(3). https://doi.org/10.1371/journal.pone.0017722

Yooseph, S., Nealson, K. H., Rusch, D. B., McCrow, J. P., Dupont, C. L., Kim, M., Johnson, J., Montgomery, R., Ferriera, S., Beeson, K., Williamson, S. J., Tovchigrechko, A., Allen, A. E., Zeigler, L. A., Sutton, G., Eisenstadt, E., Rogers, Y. H., Friedman, R., Frazier, M., & Venter, J. C. (2010). Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature, 468(7320), 60-+. https://doi.org/10.1038/Nature09530

Udwary, D. W., Zeigler, L., Asolkar, R. N., Singan, V., Lapidus, A., Fenical, W., Jensen, P. R., & Moore, B. S. (2007). Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proceedings of the National Academy of Sciences of the United States of America, 104(25), 10376–10381. https://doi.org/10.1073/pnas.0700962104

Jensen, P. R., Williams, P. G., Oh, D. C., Zeigler, L., & Fenical, W. (2007). Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora. Applied and Environmental Microbiology, 73(4), 1146–1152. https://doi.org/10.1128/aem.01891-06